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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 (BTHA-I) FROM BOTHROPS JARARACUSSU VENOM COMPLEXED WITH P-BROMOPHENACYL BROMIDE
 
Authors :  A. J. Magro, A. A. Takeda, A. M. Soares, M. R. Fontes
Date :  24 Mar 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  X-Ray Crystallography, Acidic Phospholipase A2, Bothrops Jararacussu Venom, Platelet Aggregation And Hypotensive Effects, Crystal Structure, Oligomeric State, Dimeric Phospholipase A2, Phospholipase A2 Inhibition, P- Bromophenacyl Bromide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Magro, A. A. Takeda, A. M. Soares, M. R. Fontes
Structure Of Btha-I Complexed With P-Bromophenacyl Bromide: Possible Correlations With Lack Of Pharmacological Activity.
Acta Crystallogr. , Sect. D V. 61 1670 2005
PubMed-ID: 16301802  |  Reference-DOI: 10.1107/S0907444905029598
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2
    Chains: A, B
    EC Number: 3.1.1.4
    Fragment: RESIDUES 1-133
    Organism Common: JARARACUSSU
    Organism Scientific: BOTHROPS JARARACUSSU
    Organism Taxid: 8726
    Secretion: VENOM
    Synonym: BTHA-I-PLA2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PBP2Ligand/Ion1-(4-BROMO-PHENYL)-ETHANONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , CYS A:45 , HIS A:48 , PHE B:119BINDING SITE FOR RESIDUE PBP A 1048
2AC2SOFTWAREGLY B:30 , CYS B:45 , HIS B:48 , ASP B:49BINDING SITE FOR RESIDUE PBP B 2048

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:27 -A:126
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96
8B:27 -B:126
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:91
14B:84 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z76)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2A_BOTJR59-66
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2A_BOTJR101-111
 		  2A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 1Z76)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:122
 aligned with PA2A_BOTJR | Q8AXY1 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
           PA2A_BOTJR    17 SLWQFGKMINYVMGESGVLQYLSYGCYCGLGGQGQPTDATDRCCFVHDCCYGKVTGCDPKIDSYTYSKKNGDVVCGGDDPCKKQICECDRVATTCFRDNKDTYDIKYWFYGAKNCQEKSEPC 138
               SCOP domains d1z76a_ A: automated matches                                                                                               SCOP domains
               CATH domains 1z76A00 A:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z76 A   1 SLWQFGKMINYVMGESGVLQYLSYGCYCGLGGQGQPTDATDRCCFVHDCCYGKVTGCDPKIDSYTYSKKNGDVVCGGDDPCKKQICECDRVATTCFRDNKDTYDIKYWFYGAKNCQEKSEPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  ||   131  
                                       13|                                    53|  61|                   88|                              123|        
                                        15                                     57   67                    90                               125        


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PA2A_BOTJR | Q8AXY1 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
           PA2A_BOTJR    17 SLWQFGKMINYVMGESGVLQYLSYGCYCGLGGQGQPTDATDRCCFVHDCCYGKVTGCDPKIDSYTYSKKNGDVVCGGDDPCKKQICECDRVATTCFRDNKDTYDIKYWFYGAKNCQEKSEPC 138
               SCOP domains d1z76b_ B: automated matches                                                                                               SCOP domains
               CATH domains 1z76B00 B:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z76 B   1 SLWQFGKMINYVMGESGVLQYLSYGCYCGLGGQGQPTDATDRCCFVHDCCYGKVTGCDPKIDSYTYSKKNGDVVCGGDDPCKKQICECDRVATTCFRDNKDTYDIKYWFYGAKNCQEKSEPC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  ||   131  
                                       13|                                    53|  61|                   88|                              123|        
                                        15                                     57   67                    90                               125
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z76)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PA2A_BOTJR | Q8AXY1)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008217    regulation of blood pressure    Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1z76
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  3.1.1.4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PA2A_BOTJR | Q8AXY1: 1u73 1umv 1zl7 1zlb

(-) Related Entries Specified in the PDB File

1u73 DIMERIC FORM OF NATIVE BTHA-I.
1umv MONOMERIC FORM OF NATIVE BTHA-I.